fix: granular freesurfer cache

Author: oesteban

.circleci/config.yml

@@ -55,15 +55,10 @@ jobs:
       - run:
           name: Setup git-annex
           command: |
-            mkdir -p /tmp/cache
-            if [[ ! -e "/tmp/cache/git-annex-standalone.tar.gz" ]]; then
+            if [[ ! -d /usr/lib/git-annex.linux ]]; then
               wget -O- http://neuro.debian.net/lists/trusty.us-ca.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
               apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9
               apt update && sudo apt-get install -y --no-install-recommends git-annex-standalone
-              mkdir -p /tmp/cache
-              tar czvf /tmp/cache/git-annex-standalone.tar.gz /usr/bin/git-annex /usr/bin/git-annex-shell /usr/lib/git-annex.linux
-            else
-              tar xzfv /tmp/cache/git-annex-standalone.tar.gz -C /
             fi
             git config --global user.name 'CRN'
             git config --global user.email '[email protected]'
@@ -77,6 +72,16 @@ jobs:
             python -c "from templateflow import api as tfapi; \
                        tfapi.get('MNI152NLin2009cAsym', resolution=2, desc='brain', suffix='mask'); \
                        tfapi.get('MNI152NLin2009cAsym', resolution=2, desc='fMRIPrep', suffix='boldref');"
+
+      - save_cache:
+         key: env-v1-{{ .Branch }}-{{ .BuildNum }}
+         paths:
+            - /tmp/cache/git-annex-standalone.tar.gz
+            - /usr/local/lib/python3.7/site-packages
+            - /usr/bin/git-annex
+            - /usr/bin/git-annex-shell
+            - /usr/lib/git-annex.linux
+
       - run:
           name: Install ds001600
           command: |
@@ -91,7 +96,17 @@ jobs:
                   -O testdata.zip "https://files.osf.io/v1/resources/9sy2a/providers/osfstorage/5d44b940bcd6d900198ed6be/?zip="
               unzip testdata.zip -d /tmp/data/testdata
             fi
+      - save_cache:
+         key: data-v2-{{ .Branch }}-{{ .BuildNum }}
+         paths:
+            - /tmp/data
+            - /tmp/templateflow
 
+      - restore_cache:
+          keys:
+            - freesurfer-v1-{{ .Branch }}-
+            - freesurfer-v1-master-
+            - freesurfer-v1-
       - run:
           name: Pull FreeSurfer down
           command: |
@@ -115,23 +130,12 @@ jobs:
                    --exclude='freesurfer/subjects/sample-*.mgz' \
                    --exclude='freesurfer/subjects/V1_average' \
                    --exclude='freesurfer/trctrain'
+              echo "b2VzdGViYW5Ac3RhbmZvcmQuZWR1CjMwNzU2CiAqQ1MzYkJ5VXMxdTVNCiBGU2kvUGJsejJxR1V3Cg==" | base64 -d > /tmp/freesurfer/license.txt
             fi
-      - run:
-          name: Store FreeSurfer license file
-          command: |
-            echo "b2VzdGViYW5Ac3RhbmZvcmQuZWR1CjMwNzU2CiAqQ1MzYkJ5VXMxdTVNCiBGU2kvUGJsejJxR1V3Cg==" | base64 -d > /tmp/freesurfer/license.txt
-
       - save_cache:
-         key: env-v1-{{ .Branch }}-{{ .BuildNum }}
+         key: freesurfer-v1-{{ .Branch }}-{{ .BuildNum }}
          paths:
-            - /tmp/cache/git-annex-standalone.tar.gz
-
-      - save_cache:
-         key: data-v2-{{ .Branch }}-{{ .BuildNum }}
-         paths:
-            - /tmp/data
             - /tmp/freesurfer
-            - /tmp/templateflow
 
   build_n_pytest:
     machine:
@@ -217,6 +221,11 @@ jobs:
          paths:
             - /tmp/docker
 
+      - restore_cache:
+          keys:
+            - freesurfer-v1-{{ .Branch }}-
+            - freesurfer-v1-master-
+            - freesurfer-v1-
       - restore_cache:
           keys:
             - data-v2-{{ .Branch }}-

Dockerfile

@@ -4,11 +4,6 @@ FROM ubuntu:xenial-20191010
 # Pre-cache neurodebian key
 COPY .docker/files/neurodebian.gpg /usr/local/etc/neurodebian.gpg
 
-# Installing Neurodebian packages (FSL, AFNI, git)
-RUN curl -sSL "http://neuro.debian.net/lists/$( lsb_release -c | cut -f2 ).us-ca.full" >> /etc/apt/sources.list.d/neurodebian.sources.list && \
-    apt-key add /usr/local/etc/neurodebian.gpg && \
-    (apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true)
-
 # Prepare environment
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
@@ -21,7 +16,15 @@ RUN apt-get update && \
                     autoconf \
                     libtool \
                     pkg-config \
-                    git \
+                    git && \
+    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+# Installing Neurodebian packages (FSL, AFNI, git)
+RUN curl -sSL "http://neuro.debian.net/lists/$( lsb_release -c | cut -f2 ).us-ca.full" >> /etc/apt/sources.list.d/neurodebian.sources.list && \
+    apt-key add /usr/local/etc/neurodebian.gpg && \
+    (apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true) && \
+    apt-get update && \
+    apt-get install -y --no-install-recommends \
                     fsl-core=5.0.9-5~nd16.04+1 \
                     afni=16.2.07~dfsg.1-5~nd16.04+1 \
                     convert3d \